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Related Concept Videos

DNA Microarrays02:34

DNA Microarrays

Microarrays are high-throughput and relatively inexpensive assays that can be automated to analyze large quantities of data at a time. They are used in genome-wide studies to compare gene or protein expression under two varied conditions, such as healthy and diseased states. Microarrays consist of glass or silica slides on which probe molecules are covalently attached through surface functionalization. Most commonly, the slides are prepared through the chemisorption of silanes to silica...
Comparing Copy Number Variations and SNPs02:26

Comparing Copy Number Variations and SNPs

Sequencing of the human genome has opened up several best-kept secrets of the genome. Scientists have identified thousands of genome variations that exist within a population. These variations can be a single nucleotide or a larger chromosomal variation.
Copy number variations or CNVs are the structural variations that cover more than 1kb of DNA sequence. The single nucleotide polymorphism (SNP), on the other hand, is a single nucleotide change or a point mutation that is found in more than 1%...
Single Nucleotide Polymorphisms-SNPs01:05

Single Nucleotide Polymorphisms-SNPs

A single nucleotide polymorphism or SNP is a single nucleotide variation at a specific genomic position in a large population. It is the most prevalent type of sequence variation found in the human genome. Point mutations that occur in more than 1% of the population qualify as SNPs. These are present once every 1000 nucleotides on an average in the human genome. Replacement of a purine with another purine (A/G) or a pyrimidine with another pyrimidine (C/T) is known as a transition. In contrast,...
Mismatch Repair01:20

Mismatch Repair

Organisms are capable of detecting and fixing nucleotide mismatches that occur during DNA replication. This sophisticated process requires identifying the new strand and replacing the erroneous bases with correct nucleotides. Mismatch repair is coordinated by many proteins in both prokaryotes and eukaryotes.
The Mutator Protein Family Plays a Key Role in DNA Mismatch Repair
The human genome has more than 3 billion base pairs of DNA per cell. Prior to cell division, that vast amount of genetic...
Mismatch Repair01:36

Mismatch Repair

Overview

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Related Experiment Video

Updated: Jun 18, 2026

Infinium Assay for Large-scale SNP Genotyping Applications
13:33

Infinium Assay for Large-scale SNP Genotyping Applications

Published on: November 19, 2013

Mismatch and G-stack modulated probe signals on SNP microarrays.

Hans Binder1, Mario Fasold, Torsten Glomb

  • 1Interdisciplinary Centre for Bioinformatics, Universität Leipzig, Leipzig, Germany. binder@izbi.uni-leipzig.de

Plos One
|November 20, 2009
PubMed
Summary

Sequence motifs in single nucleotide polymorphism (SNP) arrays cause systematic biases in genotyping and copy number estimates. Identifying and correcting these sequence effects, like poly-G runs, improves data accuracy.

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Candidate Gene Testing in Clinical Cohort Studies with Multiplexed Genotyping and Mass Spectrometry
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Candidate Gene Testing in Clinical Cohort Studies with Multiplexed Genotyping and Mass Spectrometry

Published on: June 21, 2018

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Last Updated: Jun 18, 2026

Infinium Assay for Large-scale SNP Genotyping Applications
13:33

Infinium Assay for Large-scale SNP Genotyping Applications

Published on: November 19, 2013

Candidate Gene Testing in Clinical Cohort Studies with Multiplexed Genotyping and Mass Spectrometry
05:53

Candidate Gene Testing in Clinical Cohort Studies with Multiplexed Genotyping and Mass Spectrometry

Published on: June 21, 2018

Area of Science:

  • Genomics
  • Bioinformatics
  • Molecular Biology

Background:

  • Single nucleotide polymorphism (SNP) arrays are crucial for genotyping and copy number estimation.
  • These arrays rely on DNA probe-target hybridization, which can be influenced by DNA sequence variations.
  • Systematic biases in SNP array data can arise from probe sequence characteristics.

Purpose of the Study:

  • To analyze probe signal variability in Affymetrix GeneChip SNP arrays.
  • To identify sequence motifs causing systematic biases in genotyping and copy number estimates.
  • To develop methods for correcting sequence-related signal effects.

Main Methods:

  • Analysis of probe signal variability as a function of probe sequence.
  • Estimation of sequence effects using triple-motif analysis (256 base pairing combinations).
  • Decomposition of probe/target interactions into nearest-neighbor contributions, correlating with DNA/DNA interaction free energy.

Main Results:

  • Probe sequence significantly modulates signal intensity, with mismatches having a larger effect than canonical pairings.
  • Runs of guanines (poly-G) and specific mismatched base pairings are identified as sources of systematic bias.
  • The poly-G effect is linked to probe crowding and complex formation.

Conclusions:

  • A model-free 'triple-averaging' method can estimate sequence motif contributions to signal intensity.
  • This method enables calibration algorithms to correct signal values for sequence effects.
  • Recommendations for sequence-based corrections are proposed to enhance data reliability.